Merge remote-tracking branch 'upstream/master'

* upstream/master:
  Move snap publishing to own workflow
  Squashed 'src/main/resources/csl-locales/' changes from 2b94bf9fac..d0ee4d13c9
  Remove obsolete step
  Add debug output for snap file location
  Try to build snapcraft image also on master-release
  Build snap only for master branch
  Update GitVersion action from v0.3 to v0.9.1 (#6061)
  Add empty line to deployment.yml to trigger build
  Release v5.0
  Refine external-libraries.txt
  Revert "Remove ci prefix for releases"
  Remove suffix "-ci.1" from version information stored in BuildInfo
  Remove ci prefix for releases
  Use github action to publish snap

Author: Siedlerchr

.github/workflows/deployment.yml

@@ -43,24 +43,16 @@ jobs:
 
     steps:
       - name: Checkout source
-        uses: actions/checkout@v2-beta
-        with:
-          fetch-depth: 0
-      - name: Fetch tags and master for GitVersion
-        run: |
-          git fetch --tags origin
-          git rev-parse --verify master
-          if (-not $?) {
-            git branch --force --create-reflog master origin/master
-          }
-        shell: pwsh
+        uses: actions/checkout@v2
+      - name: Fetch all history for all tags and branches
+        run: git fetch --prune --unshallow
       - name: Install GitVersion
-        uses: gittools/actions/setup-gitversion@v0.3
+        uses: gittools/actions/gitversion/setup@v0.9.1
         with:
-            versionSpec: '5.1.2'
+            versionSpec: '5.1.3'
       - name: Run GitVersion
         id: gitversion
-        uses: gittools/actions/execute-gitversion@v0.3
+        uses: gittools/actions/gitversion/execute@v0.9.1
       - name: Set up JDK
         uses: actions/setup-java@v1
         with:
@@ -111,25 +103,6 @@ jobs:
           export BADASS_JLINK_JPACKAGE_HOME="${GITHUB_WORKSPACE}${{ matrix.jdk14Path }}"
           ./gradlew -PprojVersion="${{ steps.gitversion.outputs.AssemblySemVer }}" -PprojVersionInfo="${{ steps.gitversion.outputs.InformationalVersion }}" jpackage
         shell: bash
-      - name: Package application image
-        run: ${{ matrix.archivePortable }}
-        shell: bash
-      - name: Build snap (1) Setup snapcraft
-        uses: jhenstridge/snapcraft-build-action@v1
-        id: snapcraft
-        if: matrix.displayName == 'linux'
-      - name: Build snap (2) Run build
-        run: |
-          mv ${{ steps.snapcraft.outputs.snap }} build/distribution/
-        if: matrix.displayName == 'linux'
-      - name: Build snap (3) Upload snap
-        if: matrix.displayName == 'linux' && github.ref == 'refs/heads/master'
-        env:
-          SNAPCRAFT_LOGIN_FILE: ${{ secrets.SNAPCRAFT_LOGIN_FILE }}
-        run: |
-            mkdir .snapcraft && echo ${SNAPCRAFT_LOGIN_FILE} | base64 --decode --ignore-garbage > .snapcraft/snapcraft.cfg
-            snapcraft push build/distribution/jabref*.snap --release edge || true
-        shell: bash
       - name: Rename files
         run: |
           get-childitem -Path build/distribution/* | rename-item -NewName {$_.name -replace "${{ steps.gitversion.outputs.AssemblySemVer }}","${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}"}
@@ -146,24 +119,16 @@ jobs:
     needs: [build]
     steps:
       - name: Checkout source
-        uses: actions/checkout@v2-beta
-        with:
-          fetch-depth: 0
-      - name: Fetch tags and master for GitVersion
-        run: |
-          git fetch --tags origin
-          git rev-parse --verify master
-          if (-not $?) {
-            git branch --force --create-reflog master origin/master
-          }
-        shell: pwsh
+        uses: actions/checkout@v2
+      - name: Fetch all history for all tags and branches
+        run: git fetch --prune --unshallow
       - name: Install GitVersion
-        uses: gittools/actions/setup-gitversion@v0.3
+        uses: gittools/actions/gitversion/setup@v0.9.1
         with:
-            versionSpec: '5.1.2'
+            versionSpec: '5.1.3'
       - name: Run GitVersion
         id: gitversion
-        uses: gittools/actions/execute-gitversion@v0.3
+        uses: gittools/actions/gitversion/execute@v0.9.1
       - name: Get linux binaries
         uses: actions/download-artifact@master
         with:
@@ -191,3 +156,4 @@ jobs:
           ssh_options: '-p 9922'
           src: 'build/distribution/'
           dest: jrrsync@build-upload.jabref.org:/var/www/builds.jabref.org/www/${{ steps.gitversion.outputs.branchName }}/
+

.github/workflows/snap.yml

@@ -0,0 +1,26 @@
+name: Snap
+
+on:
+  schedule:
+    # run on each day
+    - cron: '33 4 * * *'
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    name: Create snapcraft image
+
+    steps:
+      - name: Checkout source
+        uses: actions/checkout@v2
+      # The image relies on https://builds.jabref.org/master/JabRef-5.0-portable_linux.tar.gz^
+      # See snap/snapcraft.yml for details
+      - name: Build snap (1) Run build
+        uses: jhenstridge/snapcraft-build-action@v1
+        id: snapcraft
+      - name: Build snap (2) Upload snap
+        uses: jhenstridge/snapcraft-publish-action@v1
+        with:
+          store_login: ${{ secrets.SNAPCRAFT_LOGIN_FILE }}
+          snap: ${{ steps.snapcraft.outputs.snap }}
+          release: edge

CHANGELOG.md

@@ -9,7 +9,7 @@ Here, the categories "Changed" for added and changed functionality,
 
 We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#NUM`.
 
-## [Unreleased]
+## [5.0] – 2020-03-03
 
 ### Changed
 
@@ -284,7 +284,8 @@ The changelog of JabRef 4.x is available at the [v4.x branch](https://github.com
 The changelog of JabRef 3.x is available at the [v3.8.2 tag](https://github.com/JabRef/jabref/blob/v3.8.2/CHANGELOG.md).
 The changelog of JabRef 2.11 and all previous versions is available as [text file in the v2.11.1 tag](https://github.com/JabRef/jabref/blob/v2.11.1/CHANGELOG).
 
-[Unreleased]: https://github.com/JabRef/jabref/compare/v5.0-beta...HEAD
+[Unreleased]: https://github.com/JabRef/jabref/compare/v5.0...HEAD
+[5.0]: https://github.com/JabRef/jabref/compare/v5.0-beta...v5.0
 [5.0-beta]: https://github.com/JabRef/jabref/compare/v5.0-alpha...v5.0-beta
 [5.0-alpha]: https://github.com/JabRef/jabref/compare/v4.3...v5.0-alpha
 

GitVersion.yml

@@ -5,5 +5,5 @@ mode: ContinuousDeployment
 branches:
   master:
     regex: ^master
-    tag: beta
-    pre-release-weight: 30000 # 0 after stable release, 15000 before alpha release, 30000 before beta release, 50000 before stable release
+    tag: ''
+    pre-release-weight: 50000 # 0 after stable release, 15000 before alpha release, 30000 before beta release, 50000 before stable release

external-libraries.txt

@@ -5,6 +5,7 @@ This file is manually kept in sync with build.gradle and the binary jars contain
 
 One can list all dependencies by using Gradle task `dependencyReport`.
 It generates the file [build/reports/project/dependencies.txt](build/reports/project/dependencies.txt).
+There, [one can use](https://stackoverflow.com/a/49727249/873282) `sed 's/^.* //' | sort | uniq` to flatten the dependencies.
 
 ## Legend
 
@@ -38,30 +39,31 @@ Note:    It is important to include v1.5.54 or later as v1.5.54 is the first ver
 
 (Sorted alphabetically by Id)
 
-Id:      com.airhacks:afterburner.fx
-Project: afterburner.fx
-URL:     https://github.com/AdamBien/afterburner.fx
-License: Apache-2.0
-
-Id:      com.apple:AppleJavaExtensions
-Project: AppleJavaExtensions
-URL:     https://developer.apple.com/legacy/library/samplecode/AppleJavaExtensions/Introduction/Intro.html
-License: Apple License
-
 Id:      com.github.tomtung
 Project: latex2unicode
 URL:     https://github.com/tomtung/latex2unicode
 License: Apache-2.0
 
+Id:      com.google.code.gson:gson
+Project: Google Guava
+URL:     https://github.com/google/gson
+License: Apache-2.0
+
+Id:      com.google.guava:failureaccess
+Project: Google Guava
+URL:     https://github.com/google/guava
+License: Apache-2.0
+Note:    See https://github.com/google/guava/issues/3437 for a discussion that this dependency is really required.
+
 Id:      com.google.guava:guava
 Project: Google Guava
 URL:     https://github.com/google/guava
 License: Apache-2.0
 
-Id:      com.impossibl.pgjdbc-ng:pgjdbc-ng
-Project: pgjdbc-ng
-URL:     http://impossibl.github.io/pgjdbc-ng
-License: BSD-3-Clause
+Id:      com.google.j2objc:j2objc-annotations
+Project: j2objc-annotations
+URL:     https://github.com/google/j2objc
+License: Apache-2.0
 
 Id:      com.konghq.unirest
 Project: Unirest for Java
@@ -83,11 +85,6 @@ Project: Oracle's JDBC drivers
 URL:     https://repo1.maven.org/maven2/com/oracle/ojdbc/ojdbc10/19.3.0.0/ojdbc10-19.3.0.0.pom
 License: Oracle Free Use Terms and Conditions (FUTC)
 
-Id:      com.sibvisions.external.jvxfx:DnDTabPane
-Project: Drag'n'Drop TabPane
-URL:     https://github.com/sibvisions/javafx.DndTabPane
-License: EPL-1.0
-
 Id:      commons-cli:commons-cli
 Project: Apache Commons CLI
 URL:     http://commons.apache.org/cli/
@@ -98,11 +95,6 @@ Project: Apache Commons Logging
 URL:     http://commons.apache.org/logging/
 License: Apache-2.0
 
-Id:      de.codecentric.centerdevice
-Project: javafxsvg
-URL:     https://github.com/codecentric/javafxsvg
-License: BSD 3-Clause
-
 Id:      de.jensd:fontawesomefx-materialdesignfont
 Project: FontAwesomeFX
 URL:     https://bitbucket.org/Jerady/fontawesomefx
@@ -208,7 +200,7 @@ Project: ControlsFX
 URL:     http://fxexperience.com/controlsfx/
 License: BSD-3-Clause
 
-Id:      org.fx.misc.easybind:easybind
+Id:      org.fxmisc.easybind:easybind
 Project: EasyBind
 URL:     https://github.com/TomasMikula/EasyBind
 License: BSD-2-Clause
@@ -288,12 +280,97 @@ Project: OpenOffice.org
 URL:     http://www.openoffice.org/api/SDK
 License: Apache-2.0
 
-Id:      org.xmlunit:xmlunit-core
-Project: XMLUnit
-URL:     http://www.xmlunit.org/
-License: Apache-2.0
-
-Id:      org.xmlunit:xmlunit-matchers
-Project: XMLUnit
-URL:     http://www.xmlunit.org/
-License: Apache-2.0
+## Sorted list of runtime dependencies output by gradle
+
+```text
+com.github.tomtung:latex2unicode_2.12:0.2.6
+com.google.code.gson:gson:2.8.6
+com.google.errorprone:error_prone_annotations:2.3.4
+com.google.guava:failureaccess:1.0.1
+com.google.guava:guava:28.2-jre
+com.google.guava:listenablefuture:9999.0-empty-to-avoid-conflict-with-guava
+com.google.j2objc:j2objc-annotations:1.3
+com.ibm.icu:icu4j:62.1
+com.jfoenix:jfoenix:9.0.9
+com.konghq:unirest-java:3.6.00
+com.microsoft.azure:applicationinsights-core:2.4.1
+com.microsoft.azure:applicationinsights-logging-log4j2:2.4.1
+com.oracle.ojdbc:ojdbc10:19.3.0.0
+com.oracle.ojdbc:ons:19.3.0.0
+com.oracle.ojdbc:osdt_cert:19.3.0.0
+com.oracle.ojdbc:osdt_core:19.3.0.0
+com.oracle.ojdbc:simplefan:19.3.0.0
+com.oracle.ojdbc:ucp:19.3.0.0
+com.sun.istack:istack-commons-runtime:3.0.8
+com.sun.xml.fastinfoset:FastInfoset:1.2.16
+commons-cli:commons-cli:1.4
+commons-codec:commons-codec:1.11
+commons-logging:commons-logging:1.2
+de.jensd:fontawesomefx-commons:11.0
+de.jensd:fontawesomefx-materialdesignfont:1.7.22-11
+de.saxsys:mvvmfx-validation:1.9.0-SNAPSHOT
+de.saxsys:mvvmfx:1.8.0
+de.undercouch:citeproc-java:2.1.0-SNAPSHOT
+eu.lestard:doc-annotations:0.2
+info.debatty:java-string-similarity:1.2.1
+io.github.java-diff-utils:java-diff-utils:4.5
+jakarta.activation:jakarta.activation-api:1.2.1
+jakarta.annotation:jakarta.annotation-api:1.3.5
+jakarta.xml.bind:jakarta.xml.bind-api:2.3.2
+net.jcip:jcip-annotations:1.0
+net.jodah:typetools:0.6.1
+org.antlr:antlr-runtime:3.5.2
+org.antlr:antlr4-runtime:4.8-1
+org.apache.commons:commons-csv:1.8
+org.apache.commons:commons-lang3:3.9
+org.apache.commons:commons-text:1.8
+org.apache.httpcomponents:httpasyncclient:4.1.4
+org.apache.httpcomponents:httpclient:4.5.11
+org.apache.httpcomponents:httpcore-nio:4.4.13
+org.apache.httpcomponents:httpcore:4.4.13
+org.apache.httpcomponents:httpmime:4.5.11
+org.apache.logging.log4j:log4j-api:3.0.0-SNAPSHOT
+org.apache.logging.log4j:log4j-core:3.0.0-SNAPSHOT
+org.apache.logging.log4j:log4j-jcl:3.0.0-SNAPSHOT
+org.apache.logging.log4j:log4j-plugins:3.0.0-SNAPSHOT
+org.apache.logging.log4j:log4j-slf4j18-impl:3.0.0-SNAPSHOT
+org.apache.pdfbox:fontbox:2.0.18
+org.apache.pdfbox:pdfbox:2.0.18
+org.apache.pdfbox:xmpbox:2.0.18
+org.apache.tika:tika-core:1.23
+org.bouncycastle:bcprov-jdk15on:1.64
+org.checkerframework:checker-qual:2.10.0
+org.controlsfx:controlsfx:11.0.1
+org.fxmisc.easybind:easybind:1.0.3
+org.fxmisc.flowless:flowless:0.6.1
+org.fxmisc.richtext:richtextfx:0.10.4
+org.fxmisc.undo:undofx:2.1.0
+org.fxmisc.wellbehaved:wellbehavedfx:0.3.3
+org.glassfish.hk2.external:jakarta.inject:2.6.1
+org.glassfish.jaxb:jaxb-runtime:2.3.2
+org.glassfish.jaxb:txw2:2.3.2
+org.graalvm.js:js:19.2.1
+org.graalvm.regex:regex:19.2.1
+org.graalvm.sdk:graal-sdk:19.2.1
+org.graalvm.truffle:truffle-api:19.2.1
+org.jbibtex:jbibtex:1.0.17
+org.jsoup:jsoup:1.13.1
+org.jvnet.staxex:stax-ex:1.8.1
+org.mariadb.jdbc:mariadb-java-client:2.5.4
+org.openjfx:javafx-base:13.0.2
+org.openjfx:javafx-controls:13.0.2
+org.openjfx:javafx-fxml:13.0.2
+org.openjfx:javafx-graphics:13.0.2
+org.openjfx:javafx-media:13.0.2
+org.openjfx:javafx-swing:13.0.2
+org.openjfx:javafx-web:13.0.2
+org.ow2.asm:asm-analysis:6.2.1
+org.ow2.asm:asm-commons:6.2.1
+org.ow2.asm:asm-tree:6.2.1
+org.ow2.asm:asm-util:6.2.1
+org.ow2.asm:asm:6.2.1
+org.postgresql:postgresql:42.2.10
+org.reactfx:reactfx:2.0-M5
+org.scala-lang:scala-library:2.12.8
+org.slf4j:slf4j-api:2.0.0-alpha1
+```

src/main/java/org/jabref/logic/util/Version.java

@@ -29,8 +29,9 @@ public class Version {
     private static final Version UNKNOWN_VERSION = new Version();
 
     private final static Pattern VERSION_PATTERN = Pattern.compile("(?<major>\\d+)(\\.(?<minor>\\d+))?(\\.(?<patch>\\d+))?(?<stage>-alpha|-beta)?(?<dev>-?dev)?.*");
-    private static final String JABREF_GITHUB_RELEASES = "https://api.github.com/repos/JabRef/JabRef/releases";
+    private final static Pattern CI_SUFFIX_PATTERN = Pattern.compile("-ci\\.\\d+$");
 
+    private static final String JABREF_GITHUB_RELEASES = "https://api.github.com/repos/JabRef/JabRef/releases";
 
     private String fullVersion = BuildInfo.UNKNOWN_VERSION;
     private int major = -1;
@@ -58,6 +59,10 @@ public static Version parse(String version) {
 
         Version parsedVersion = new Version();
 
+        // remove "-ci.1" suffix
+        Matcher ciSuffixMatcher = CI_SUFFIX_PATTERN.matcher(version);
+        version = ciSuffixMatcher.replaceAll("");
+
         parsedVersion.fullVersion = version;
         Matcher matcher = VERSION_PATTERN.matcher(version);
         if (matcher.find()) {
@@ -277,7 +282,7 @@ public static DevelopmentStage parse(String stage) {
             } else if (stage.equals(BETA.stage)) {
                 return BETA;
             }
-            LOGGER.warn("Unknown development stage: " + stage);
+            LOGGER.warn("Unknown development stage: {}", stage);
             return UNKNOWN;
         }
 

src/main/resources/csl-locales/CONTRIBUTING.md

@@ -4,14 +4,14 @@ We welcome contributions to the Citation Style Language (CSL) locale files in th
 
 The CSL locale files provide the standard translations for automatic localization of CSL styles.
 As such, the CSL locale files should generally contain the most commonly used translations for a given locale.
-Less common translations can be [provided in the individual CSL styles](http://docs.citationstyles.org/en/stable/specification.html#locale) that require them, which will overwrite the CSL locale file translations.
+Less common translations can be [provided in the individual CSL styles](https://docs.citationstyles.org/en/stable/specification.html#locale) that require them, which will overwrite the CSL locale file translations.
 
 Because each CSL locale file offers the standard translations for all CSL styles, changes should be made conservatively and carefully.
 We will often ask a second native speaker and/or past contributor to look over your proposed changes.
 
 ## Licensing and crediting
 
-By creating a pull request, you agree to license your contributions under the [Creative Commons Attribution-ShareAlike 3.0 Unported license](http://creativecommons.org/licenses/by-sa/3.0/) license.
+By creating a pull request, you agree to license your contributions under the [Creative Commons Attribution-ShareAlike 3.0 Unported license](https://creativecommons.org/licenses/by-sa/3.0/) license.
 
 In addition, if you're interested in being credited, please add yourself to the locale file as translator. See the example below (both the `<email/>` and `</uri>` elements are optional):
 

src/test/java/org/jabref/logic/util/VersionTest.java

@@ -282,4 +282,10 @@ public void alphaShouldBeUpdatedToStables() {
         List<Version> availableVersions = Arrays.asList(Version.parse("2.8-beta"), stable);
         assertEquals(Optional.of(stable), alpha.shouldBeUpdatedTo(availableVersions));
     }
+
+    @Test
+    public void ciSuffixShouldBeRemoved() {
+        Version v50ci = Version.parse("5.0-ci.1");
+        assertEquals("5.0", v50ci.getFullVersion());
+    }
 }